Hi @Saif,
Check out this great forum post regarding whether to trim inside or outside of QIIME 2 - I would say that unless you have a very specific reason for trimming outside of QIIME 2, I would recommend doing it in QIIME 2 (especially if you are doing more analysis downstream within QIIME 2). Any action you perform within QIIME 2 will be recorded in the resulting artifacts/visualizations, and will thus be easy for future folks to review and replicate if needed (yourself included).
If you're just trimming based on quality scores, that can absolutely be done within QIIME 2 using the q2-dada2 plugin. You can use your demux summary to take a look at the interactive quality plot to make sure you're trimming/truncating at the correct bp location(s).
Hope this helps! Cheers 